Fig. 2: RBFOX2 recruits m6A MTC to gene promoter for RNA methylation.
a, Cumulative curve and box plot (inset) of m6A log2(fold change (FC)) comparing RBFOX2 KD (shRBFOX2) versus control (shNS) K562 cells. m6A peaks (N) were categorized into two groups according to whether they overlapped with RBFOX2 peaks (+, N = 5,089) or not (−, N = 23,381) (refs. 29,30). b, Cumulative curve and box plot (inset) of RNA log2FC comparing RBFOX2 KD versus control K562 cells. caRNAs (N) were categorized into two groups according to whether they are derived from regions with RBFOX2 binding (+, N = 5,089) or not (−, N = 23,381) (refs. 29,30). c, Western blots of the immunoprecipitated RBFOX2 from K562 cells and its interactions with METTL3, METTL14 and RBM15 after RNase A/T1 treatment. d, Venn diagram of overlap between RBFOX2 ChIP–seq and RBM15 eCLIP peaks in K562 cells29,30. Two-sided P value was calculated by Fisher’s exact test. e, Average profile of RBFOX2 binding intensity at RBFOX2 peak centres and the flanking 2.5 kb regions in K562 cells. RBFOX2 peaks were categorized into two groups according to whether they overlap with RBM15 eCLIP peaks (+) or not (−)29,30. f, Box plot of m6A log2FC comparing RBFOX2 KD versus control K562 cells. m6A peaks (N) were categorized into three groups according to whether they overlapped with RBFOX2 or RBM15 peaks29,30. From left to right, N = 22,061, 4,049 and 1,040. g, Average profile of RBM15 binding intensity at RBFOX2 peak centres and the flanking 2.5 kb regions in K562 cells. RBM15 peaks were categorized into two groups according to whether they overlap with RBFOX2 (+) or not (−) (refs. 29,30). h, The integrative genomics viewer plots showing RBFOX2 ChIP–seq signals in wild-type K562 cells29,30, and RBM15 ChIP–seq signals in control and RBFOX2 KD K562 cells around H2AC8/H2BC8 (left) and SOCS1 (right) gene loci.
